<PAGE>   1
 
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                                 UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549
 
                             ---------------------
 
                                  FORM 10-K/A
                               (Amendment No. 1)
 
(Mark One)
     [X]        ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF
                      THE SECURITIES EXCHANGE ACT OF 1934
 
                  FOR THE FISCAL YEAR ENDED DECEMBER 31, 1998
 
                                       OR
 
     [ ]      TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF
                      THE SECURITIES EXCHANGE ACT OF 1934
 
       FOR THE TRANSITION PERIOD FROM                TO                .
 
                         COMMISSION FILE NUMBER 1-2700
 
                          EL PASO NATURAL GAS COMPANY
             (Exact Name of Registrant as Specified in Its Charter)
 
<TABLE>
<S>                                                 <C>
                     DELAWARE                                           74-0608280
         (State or Other Jurisdiction of                             (I.R.S. Employer
          Incorporation or Organization)                           Identification No.)
 
             EL PASO ENERGY BUILDING
              1001 LOUISIANA STREET
                  HOUSTON, TEXAS                                          77002
     (Address of Principal Executive Offices)                           (Zip Code)
</TABLE>
 
       REGISTRANT'S TELEPHONE NUMBER, INCLUDING AREA CODE: (713) 420-2131
 
          SECURITIES REGISTERED PURSUANT TO SECTION 12(b) OF THE ACT:
 
<TABLE>
<CAPTION>
                                                    NAME OF EACH EXCHANGE
         TITLE OF EACH CLASS                         ON WHICH REGISTERED
         -------------------                        ---------------------
<S>                                     <C>
9.45% Notes due 1999..................  New York Stock Exchange
</TABLE>
 
        SECURITIES REGISTERED PURSUANT TO SECTION 12(g) OF THE ACT: NONE
 
     Indicate by check mark whether the registrant (1) has filed all reports
required to be filed by Section 13 or 15(d) of the Securities Exchange Act of
1934 during the preceding 12 months (or for such shorter period that the
registrant was required to file such reports), and (2) has been subject to such
filing requirements for the past 90 days. Yes  [X]  No  [ ].
 
     Indicate by check mark if disclosure of delinquent filers pursuant to Item
405 of Regulation S-K is not contained herein, and will not be contained, to the
best of registrant's knowledge, in definitive proxy or information statements
incorporated by reference in Part III of this Form 10-K or any amendment to this
Form 10-K.  [X]
 
     STATE THE AGGREGATE MARKET VALUE OF THE VOTING STOCK HELD BY NON-AFFILIATES
OF THE REGISTRANT...........................................................NONE
 
     INDICATE THE NUMBER OF SHARES OUTSTANDING OF EACH OF THE REGISTRANT'S
CLASSES OF COMMON STOCK, AS OF THE LATEST PRACTICABLE DATE.
 
     Common Stock, par value $1 per share. Shares outstanding on March 16, 1999:
1,000
 
     EL PASO NATURAL GAS COMPANY MEETS THE CONDITIONS OF GENERAL INSTRUCTION
I(1)(a) AND (b) TO FORM 10-K AND IS THEREFORE FILING THIS REPORT WITH A REDUCED
DISCLOSURE FORMAT AS PERMITTED BY SUCH INSTRUCTION.
 
                   DOCUMENTS INCORPORATED BY REFERENCE: NONE
 
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
<PAGE>   2
 
                          EL PASO NATURAL GAS COMPANY
                                EXPLANATORY NOTE
 
     El Paso Natural Gas Company hereby amends its Annual Report on Form 10-K
for the year ended December 31, 1998, to include for the following periods
Restated Financial Data Schedules as a result of a tax-free internal
reorganization effected by the parent company, El Paso Energy Corporation:
 
Year Ended December 31, 1997
Year Ended December 31, 1996
Quarter Ended March 31, 1998
Quarter Ended June 30, 1998
Quarter Ended September 30, 1998
Quarter Ended March 31, 1997
Quarter Ended June 30, 1997
Quarter Ended September 30, 1997
 
     Accordingly, the undersigned hereby amends the Exhibit Index of its Annual
Report on Form 10-K for the year ended December 31, 1998, by inserting in the
Exhibit Index Exhibits 27(2) through 27(9) filed herewith. All exhibits other
than Exhibits 27(2) through 27(9) that are marked with an asterisk (*) in the
Exhibit List were filed with the registrant's Form 10-K on March 22, 1999.
<PAGE>   3
 
                                   SIGNATURES
 
     Pursuant to the requirements of the Securities Exchange Act of 1934, the
registrant has duly caused this amendment to be signed on its behalf by the
undersigned, thereunto duly authorized.
 
<TABLE>
<S>                                            <C>
                                               EL PASO NATURAL GAS COMPANY
 
Date: April 5, 1999                                        /s/ JEFFREY I. BEASON
                                               ----------------------------------------------
                                                             Jeffrey I. Beason
                                                       Vice President and Controller
                                                         (Chief Accounting Officer)
</TABLE>
<PAGE>   4
 
                          EL PASO NATURAL GAS COMPANY
 
                                  EXHIBIT LIST
                               DECEMBER 31, 1998
 
     Exhibits not incorporated by reference to a prior filing are designated by
an asterisk. All exhibits not so designated are incorporated herein by reference
to a prior filing as indicated.
 
   
<TABLE>
<CAPTION>
        EXHIBIT
         NUMBER                                  DESCRIPTION
        -------                                  -----------
<C>                      <S>
          2              -- Amended and Restated Merger Agreement dated as of June
                            19, 1996 by and among EPNG, El Paso Merger Company and
                            EPTPC (Exhibit 2.A to EPNG's Registration Statement on
                            Form S-4, filed August 27, 1996, File No. 333-10911).
         *3.A            -- Restated Certificate of Incorporation of EPNG dated
                            August 3, 1998 as amended.
          3.B            -- By-laws of EPNG, as amended October 22, 1997 (Exhibit 3.B
                            to EPNG's Form 10-Q, filed November 13, 1997, File No.
                            1-2700).
         *4.A            -- Indenture dated as of January 1, 1992, between EPNG and
                            Citibank, N.A., Trustee with respect to 7 3/4% Notes due
                            2002 and 8 5/8% Debentures due 2022.
          4.B            -- Indenture dated as of November 13, 1996, between EPNG and
                            The Chase Manhattan Bank, as Trustee, (Exhibit 4.1 to
                            EPNG's Form 8-K, filed November 13, 1996, File No.
                            1-2700); Form of 6 3/4% Notes Due 2003, (Exhibit 4.2 to
                            EPNG's Form 8-K, filed November 13, 1996, File No.
                            1-2700); Form of 7 1/2% Debentures Due 2026 (Exhibit 4.2
                            to EPNG's Form 8-K, filed November 13, 1996, File No.
                            1-2700).
         10.A            -- $750 million 364-Day Revolving Credit and Competitive
                            Advance Facility Agreement dated as of October 29, 1997,
                            by and among EPNG, TGP, The Chase Manhattan Bank,
                            Citibank, N.A., Morgan Guaranty Trust Company of New
                            York, and certain other banks (Exhibit 10.A to EPEC's
                            Form 10-Q, filed November 12, 1998, File No. 1-143650
                            (the "EPEC 1998 Third Quarter 10-Q")); First Amendment to
                            the $750 million 364-Day Revolving Credit and Competitive
                            Advance Facility dated as of October 9, 1998, among EPNG,
                            TGP, The Chase Manhattan Bank, Citibank, N.A., Morgan
                            Guaranty Trust Company of New York, and certain other
                            banks (Exhibit 10.B to the EPEC 1998 Third Quarter 10-Q).
         10.B            -- $750 million 5-Year Revolving Credit and Competitive
                            Advance Facility Agreement dated as of October 29, 1997,
                            by and among EPNG, TGP, The Chase Manhattan Bank,
                            Citibank, N.A., Morgan Guaranty Trust Company of New
                            York, and certain other banks (Exhibit 10.D to the EPEC
                            1998 Third Quarter 10-Q); First Amendment to the $750
                            million 5-Year Revolving Credit and Competitive Advance
                            Facility dated as of October 9, 1998, among EPNG, TGP,
                            The Chase Manhattan Bank, Citibank, N.A., Morgan Guaranty
                            Trust Company of New York, and certain other banks
                            (Exhibit 10.E to the EPEC 1998 Third Quarter 10-Q).
        *18              -- Letter Regarding Change in Accounting Principles.
         21              -- Omitted pursuant to the reduced disclosure format
                            permitted by General Instruction I to Form 10-K.
        *27(1)           -- Financial Data Schedule for the Year ended December 31,
                            1998.
        *27(2)           -- Financial Data Schedule for the Year Ended December 31,
                            1997.
        *27(3)           -- Financial Data Schedule for the Year Ended December 31,
                            1996.
        *27(4)           -- Financial Data Schedule for the Quarter Ended March 31,
                            1998.
        *27(5)           -- Financial Data Schedule for the Quarter Ended June 30,
                            1998.
        *27(6)           -- Financial Data Schedule for the Quarter Ended September
                            30, 1998.
        *27(7)           -- Financial Data Schedule for the Quarter Ended March 31,
                            1997.
        *27(8)           -- Financial Data Schedule for the Quarter Ended June 30,
                            1997.
        *27(9)           -- Financial Data Schedule for the Quarter Ended September
                            30, 1997.
</TABLE>
    
<PAGE>   5
 
UNDERTAKING.
 
     The undersigned Registrant hereby undertakes, pursuant to Regulation S-K,
Item 601(b), paragraph (4)(iii), to furnish to the Securities and Exchange
Commission upon request all constituent instruments defining the rights of
holders of long-term debt of Registrant and its consolidated subsidiaries not
filed herewith for the reason that the total amount of securities authorized
under any of such instruments does not exceed 10 percent of the total
consolidated assets of Registrant and its consolidated subsidiaries.